Hi Christoph,
Thank you for your prompt response. Actually, i am not able to understand
the following lines:
csg_get_interaction_property: No value for 'inverse.lammps.table_bins'
found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_interaction_property: returning emtpy value for
'inverse.lammps.table_bins'
csg_get_interaction_property: No value for 'inverse.lammps.table_begin'
found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
csg_get_interaction_property: returning emtpy value for
'inverse.lammps.table_begin'
I have given the values of table_bins, table_begin, in my bond.xml file.
But, i don't think csg_call is reading these values from there. And same is
the case for lammps.scale and lammps.y_scale. Why csg_call is taking the
default values, if the values for these parameters are already given in
bond.xml file.
And furthermore, what is the meaning of scriptpath in the following lines.
csg_get_property: No value for 'cg.inverse.scriptpath' found in bond.xml,
trying /usr/share/votca/xml/csg_defaults.xml
csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
Thank you.
Sanjeet
On Fri, Sep 9, 2022 at 6:34 PM Christoph Junghans <[email protected]>
wrote:
> On Fri, Sep 9, 2022 at 1:06 PM Sanjeet Singh <[email protected]> wrote:
> >
> > Hi Christoph,
> >
> > I am trying to convert the bonded potential to LAMMPS table. For this, i
> am using the following command:
> >
> > csg_call --ia-type bond --ia-name bond-AB --options bond.xml
> convert_potential lammps --clean input_bond-AB.pot table_AB.xvg
> >
> > I am able to get the final output file table_AB.xvg.
> >
> > But, i am not able to understand the following lines on TERMINAL.
> >
> > csg_get_property: No value for 'cg.inverse.scriptpath' found in
> bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_property: returning emtpy value for 'cg.inverse.scriptpath'
> > We are using Sim Program: lammps
> > Running subscript 'potential_to_lammps.sh --clean input_bond-AB.pot
> ./TABLE/table_AB.xvg' (from tags convert_potential lammps) dir
> /usr/share/votca/scripts/inverse
> > Convert input_bond-AB.pot to ./TABLE/table_AB.xvg
> > csg_get_interaction_property: No value for 'inverse.lammps.table_bins'
> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: returning emtpy value for
> 'inverse.lammps.table_bins'
> > csg_get_interaction_property: No value for 'inverse.lammps.table_begin'
> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: returning emtpy value for
> 'inverse.lammps.table_begin'
> > csg_get_interaction_property: No value for 'inverse.lammps.table_end'
> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: returning emtpy value for
> 'inverse.lammps.table_end'
> > csg_get_interaction_property: No value for 'inverse.lammps.scale' found
> in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: value for 'inverse.lammps.scale' from
> /usr/share/votca/xml/csg_defaults.xml: 1
> > csg_get_interaction_property: No value for 'inverse.lammps.y_scale'
> found in bond.xml, trying /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: value for 'inverse.lammps.y_scale' from
> /usr/share/votca/xml/csg_defaults.xml: 1
> > Running critical command 'mktemp input_bond-AB.pot.smooth.XXXXX'
> > Running critical command 'csg_resample --in input_bond-AB.pot --out
> input_bond-AB.pot.smooth.I7rqa --grid 0:0.001:1.0'
> > Running critical command 'mktemp input_bond-AB.pot.extrapol.XXXXX'
> > csg_get_interaction_property: No value for
> 'inverse.lammps.table_left_extrapolation' found in bond.xml, trying
> /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: returning emtpy value for
> 'inverse.lammps.table_left_extrapolation'
> > csg_get_interaction_property: No value for
> 'inverse.lammps.table_right_extrapolation' found in bond.xml, trying
> /usr/share/votca/xml/csg_defaults.xml
> > csg_get_interaction_property: returning emtpy value for
> 'inverse.lammps.table_right_extrapolation'
> > Running subscript 'potential_extrapolate.sh --clean --type bond
> input_bond-AB.pot.smooth.I7rqa input_bond-AB.pot.extrapol.IjNh9' (from tags
> potential extrapolate) dir /usr/share/votca/scripts/inverse
> > Extrapolate input_bond-AB.pot.smooth.I7rqa to
> input_bond-AB.pot.extrapol.IjNh9
> > Running critical command 'mktemp
> input_bond-AB.pot.smooth.I7rqa.onlyleft.XXXXX'
> > Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
> --region left input_bond-AB.pot.smooth.I7rqa
> input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj' (from tags table
> extrapolate) dir /usr/share/votca/scripts/inverse
> > table_extrapolate.pl: extrapolating the left using linear with gradient
> -2509.86163466666
> > Running subscript 'table_extrapolate.pl --function linear --avgpoints 3
> --region right input_bond-AB.pot.smooth.I7rqa.onlyleft.FDhHj
> input_bond-AB.pot.extrapol.IjNh9' (from tags table extrapolate) dir
> /usr/share/votca/scripts/inverse
> > table_extrapolate.pl: extrapolating the right using linear with
> gradient 2241.54540033333
> > Running critical command 'mktemp input_bond-AB.pot.interpol.XXXXX'
> > Running critical command 'mktemp input_bond-AB.pot.deriv.XXXXX'
> > Running critical command 'csg_resample --in
> input_bond-AB.pot.extrapol.IjNh9 --out input_bond-AB.pot.interpol.LyEum
> --grid 0:0.001:1.0 --der input_bond-AB.pot.deriv.TAbSL --comment Created on
> Fri Sep 9 03:02:09 PM EDT 2022 by sanjeetsingh@fedora
> > called from potential_to_lammps.sh, version 2022-dev
> > settings file:
> '/home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL/bond.xml'
> > working directory:
> /home/sanjeetsingh/Documents/SANJEET-PEO/PEO-TRIAL/MAPPING-TRIAL/RDF-GENERATION/BONDED-POTENTIAL'
> > Running critical command 'mktemp input_bond-AB.pot.shift.XXXXX'
> > Running subscript 'potential_shift.pl --type bond
> input_bond-AB.pot.interpol.LyEum input_bond-AB.pot.shift.moz4C' (from tags
> potential shift) dir /usr/share/votca/scripts/inverse
> > Running subscript 'table_to_tab.pl --header lammps --type bond
> input_bond-AB.pot.shift.moz4C input_bond-AB.pot.deriv.TAbSL
> ./TABLE/table_AB.xvg' (from tags convert_potential tab) dir
> /usr/share/votca/scripts/inverse
> >
> > I mean, am i doing any mistake?
> Is there an error? I don't see any error message above.
> Just have a look at table_AB.xvg. The output above is mainly, so you
> can see all the sub steps that have done.
>
> In short lines starting with "csg_get_interaction_property" read
> values from your xml file (or use the default if empty)
> Line with "Running subscript .." run a sub step e.g. interpolation,
> extrapolation
>
> Christoph
>
> >
> > I am attaching my bond.xml file here.
> >
> > Can you please help me with this.
> >
> > Thank you.
> >
> > Sanjeet
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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> .
>
--
*Sanjeet Kumar Singh*
*Postdoctoral Fellow*
*LPCM Lab.*
*University De Sherbrooke*
*Sherbrooke, Canada.*
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<cg>
<bonded>
<!-- name of the interaction -->
<name>bond-AB</name>
<min>0</min>
<max>1.0</max>
<step>0.001</step>
</bonded>
<inverse>
<program> lammps </program>
<lammps>
<!-- name of the table for lammps run -->
<table>CG-BOND-AB.pot</table>
<!-- nm to angstrom -->
<scale>10</scale>
<!-- kJ/mol to kcal/mol -->
<y_scale>0.239006</y_scale>
<table_begin>0.20</table_begin>
<table_bins>0.001</table_bins>
</lammps>
</inverse>
</cg>
